How do I prepare my students for tornado and handle fear? We duck and cover so I can't comfort them well.

Calm reassurance. This is a situation where fear is a natural response. Calm reassurance on your part and distraction, if possible, singing, some sort of naming game, etc., are the best available tools at the time. Practicing in advance with clear explanation of what they are doing and why also can be a big help if thte actual event occurs.